One of the things I love most about the Nolanverse is how Gotham City is a richly populated city full of different characters and villains. There is no one central villain, there is a population
of them. I think having the Scarecrow re-appear for a cameo in The Dark Knight
was important and integral to the plot because it showed the vastness of the world that Batman inhabits; just because a character/villain appears, and disappears, does not mean that is the end of him or her.
Both Batman Begins
and The Dark Knight
succeed at dealing with multiple villains. You have Ra's al Ghul, the Scarecrow and Carmine Falcone, and then The Joker, Two-Face and Sal Maroni (who represented the mob element, which I liked, verses just Falcone as the mob head and that's it, we had Maroni, the Chechen, Gambol...). All of these characters flow effortlessly and seamlessly into the plot of each film and serve a purpose, not only plot-wise but thematically as well. Ra's al Ghul was central to Bruce's story, the Scarecrow was central to the theme of fear, and Joker & Two-Face both encapsulated that film's themes of the thin line between anarchy and order and the triumph of evil over good.